5A61

Crystal structure of full-length E. coli ygiF in complex with tripolyphosphate and two manganese ions.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

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This is version 1.2 of the entry. See complete history


Literature

Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes.

Martinez, J.Truffault, V.Hothorn, M.

(2015) J Biol Chem 290: 23348

  • DOI: 10.1074/jbc.M115.674473
  • Primary Citation of Related Structures:  
    5A5Y, 5A60, 5A61, 5A64, 5A65, 5A66, 5A67, 5A68

  • PubMed Abstract: 
  • Triphosphate tunnel metalloenzymes (TTMs) are present in all kingdoms of life and catalyze diverse enzymatic reactions such as mRNA capping, the cyclization of adenosine triphosphate, the hydrolysis of thiamine triphosphate, and the synthesis and breakdown of inorganic polyphosphates ...

    Triphosphate tunnel metalloenzymes (TTMs) are present in all kingdoms of life and catalyze diverse enzymatic reactions such as mRNA capping, the cyclization of adenosine triphosphate, the hydrolysis of thiamine triphosphate, and the synthesis and breakdown of inorganic polyphosphates. TTMs have an unusual tunnel domain fold that harbors substrate- and metal co-factor binding sites. It is presently poorly understood how TTMs specifically sense different triphosphate-containing substrates and how catalysis occurs in the tunnel center. Here we describe substrate-bound structures of inorganic polyphosphatases from Arabidopsis and Escherichia coli, which reveal an unorthodox yet conserved mode of triphosphate and metal co-factor binding. We identify two metal binding sites in these enzymes, with one co-factor involved in substrate coordination and the other in catalysis. Structural comparisons with a substrate- and product-bound mammalian thiamine triphosphatase and with previously reported structures of mRNA capping enzymes, adenylate cyclases, and polyphosphate polymerases suggest that directionality of substrate binding defines TTM catalytic activity. Our work provides insight into the evolution and functional diversification of an ancient enzyme family.


    Organizational Affiliation

    From the Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland and michael.hothorn@unige.ch.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INORGANIC TRIPHOSPHATASEA435Escherichia coli K-12Mutation(s): 0 
Gene Names: ygiFb3054JW3026
EC: 3.6.1.25
UniProt
Find proteins for P30871 (Escherichia coli (strain K12))
Explore P30871 
Go to UniProtKB:  P30871
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.676α = 90
b = 89.676β = 90
c = 125.329γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2015-10-07
    Changes: Database references